Upload UCE 33-layer model

.gitattributes

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 *.zip filter=lfs diff=lfs merge=lfs -text
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+new_species_protein_embeddings.csv filter=lfs diff=lfs merge=lfs -text

README.md

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+# UCE 33LAYER Model
+
+## Model Information
+
+- **Model**: Universal Cell Embeddings (UCE)
+- **Variant**: 33-layer Transformer
+- **Source**: https://github.com/snap-stanford/UCE
+- **Paper**: [Universal Cell Embeddings: A Foundation Model for Cell Biology](https://www.biorxiv.org/content/10.1101/2023.11.28.568918v1)
+
+## Architecture
+
+- **Layers**: 33
+- **Model Dimension**: 1280
+- **Attention Heads**: 20
+- **Hidden Dimension**: 5120
+- **Output Dimension**: 1280
+- **Token Dimension**: 5120 (ESM2 protein embeddings)
+
+## Usage
+
+```python
+from perturblab.model.uce import UCEModel
+
+# Load pretrained model
+model = UCEModel.from_pretrained('./weights/uce-33layer')
+
+# Generate embeddings
+result = model.predict_embeddings(
+    data=adata,  # or PerturbationData
+    species='human',
+    batch_size=25
+)
+
+cell_embeddings = result['cell_embeddings']  # (n_cells, 1280)
+gene_embeddings = result['gene_embeddings']  # (n_cells, seq_len, 1280)
+```
+
+## Files
+
+- `model.pt`: Model state dict
+- `tokens.pt`: Token embeddings (ESM2-650M + chromosome tokens)
+- `config.json`: Model configuration
+- `species_chrom.csv`: Gene to chromosome mapping
+- `species_offsets.pkl`: Species offsets in token file
+- `protein_embeddings/`: Protein embeddings for each species
+- `README.md`: This file
+
+## Citation
+
+```bibtex
+@article{rosen2023universal,
+  title={Universal Cell Embeddings: A Foundation Model for Cell Biology},
+  author={Rosen, Yanay and Roohani, Yusuf and Agrawal, Ayush and Samotorcan, Leon and Consortium, Tabula Sapiens and Quake, Stephen R and Leskovec, Jure},
+  journal={bioRxiv},
+  pages={2023--11},
+  year={2023},
+  publisher={Cold Spring Harbor Laboratory}
+}
+```
+
+## License
+
+MIT License (see original repository for details)

config.json

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+{
+  "model_series": "uce",
+  "model_name": "33layer",
+  "model_type": "embedding_extractor",
+  "nlayers": 33,
+  "d_model": 1280,
+  "nhead": 20,
+  "d_hid": 5120,
+  "output_dim": 1280,
+  "token_dim": 5120,
+  "dropout": 0.05,
+  "pad_length": 1536,
+  "sample_size": 1024,
+  "pad_token_idx": 0,
+  "chrom_token_left_idx": 1,
+  "chrom_token_right_idx": 2,
+  "cls_token_idx": 3,
+  "CHROM_TOKEN_OFFSET": 143574,
+  "species": "human",
+  "embedding_model": "ESM2",
+  "spec_chrom_csv_path": "species_chrom.csv",
+  "token_file": "tokens.pt",
+  "protein_embeddings_dir": "protein_embeddings/",
+  "offset_pkl_path": "species_offsets.pkl",
+  "batch_first": true
+}

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